Jump to main content
Jump to site search

Issue 33, 2010
Previous Article Next Article

A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

Author affiliations

Abstract

Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosineguanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G, which lacks aromatic side rings.

Graphical abstract: A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

Back to tab navigation

Supplementary files

Publication details

The article was received on 09 Mar 2010, accepted on 21 May 2010 and first published on 09 Jun 2010


Article type: Paper
DOI: 10.1039/C004020G
Phys. Chem. Chem. Phys., 2010,12, 9677-9684

  •   Request permissions

    A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

    M. Kabeláč, F. Zimandl, T. Fessl, Z. Chval and F. Lankaš, Phys. Chem. Chem. Phys., 2010, 12, 9677
    DOI: 10.1039/C004020G

Search articles by author

Spotlight

Advertisements